In 2006, Bruno was signed by investment fund Media Sports Investments, which has been linked to various transactions with Atlético-MG; the deal was speculated to have been worth around € 2 million, plus 15% on a future deal.[5] He went on to sign a contract, until the end of the year, with Corinthians, then a partner of MSI. However, following manager Émerson Leão's continuous refusal to play Bruno over home-grown keeper Marcelo, Bruno became deeply unsatisfied. With no match played for Corinthians, he was loaned out to Flamengo.

At his new side, Bruno arrived in the same week Diego, the first team goalkeeper at the time, suffered an injury. He instantly replaced incumbent Diego as first choice goalkeeper. He made his début in a match against Internacional and then delivered some impressive performances, cementing his starting position between the posts for the rest of the season. In 2007, he became a fan favourite for his great showings, specially on penalties, by making three saves in the Rio de Janeiro State Championship 2007 finals against Botafogo, helping Flamengo become the champions. Throughout the year, it was speculated that Bruno would depart for Europe, with MSI wishing to cash-in on him, and the goalkeeper was linked with Barcelona.[6]

For around €3million, Flamengo sealed a permanent deal with Bruno in 2008,[7] with the player stating his desire to be with the rubro-negro for the foreseeable future. Bruno scored his first professional goal on 23 April 2008, from a free kick, which led the way for a crucial 2–0 victory over Coronel Bolognesi in the Copa Libertadores.[8] Bruno scored his second goal on 23 October 2008, in a penalty kick against Coritiba.[9] He scored his third goal for Flamengo on 4 February 2009, in a free kick, against Mesquita.[10]

His fourth career goal, this time from a free kick, was for Flamengo on 26 May 2010, in a Campeonato Brasileiro match which they lost 2–1 to Fluminense.[11]

In July 2010, Flamengo announced the club had suspended Bruno's contract as a result of the murder investigation and the club lawyer would no longer act in his defence.[12] In September 2010 according to news report Bruno had tried to commit suicide twice while in prison waiting for his trial to begin.[13]

On 9 June 2010, the athlete's former girlfriend, Eliza Samudio, disappeared.[16] In July 2010, a Brazilian judge ordered his arrest in connection with her disappearance.[17] A cousin of Fernandes de Souza told police that he had taken part in Samudio's abduction with his friend, Luiz Henrique Ferreira Romao. He also stated that Samudio was dead but did not say how she died, nor where her body was, and that Fernandes de Souza was the father of her baby despite him being married.[18] Since then he has lost the club's captaincy, Flamengo have also suspended his contract with the club while the club's lawyer will no longer be representing him in court.

In late July, he was formally charged with murder, kidnapping, hiding a body, forming a criminal gang (conspiracy) and corrupting minors.[19] According to police, Bruno's teenage cousin stated that Samudio's body was cut up and some parts were fed to dogs, while other parts were buried under concrete.[1] The case has led to debate in Brazil concerning misbehavior by professional athletes and growing crime against women.[20]